Single-cell transcriptome analysis reveals regulatory programs of prognosis-associated RNA binding proteins during...

Hepatocellular carcinoma (HCC), a highly aggressive primary liver cancer, exhibits unclear heterogeneity in RNA-binding protein (RBP) expression dynamics. This study investigates single-cell-level RBP heterogeneity, regulatory roles in HCC progression, and their therapeutic potential.

Utilizing TCGA-LIHC data, prognosis-associated RBPs were screened by univariate Cox analysis. Tumor clusters stratified via NMF algorithm underwent differential gene expression profiling and functional enrichment (GO/KEGG). Single-cell RNA sequencing dissected RBP heterogeneity in malignant and myeloid-derived cell populations, exploring intercellular interactions. Key RBP gene HDGF was functionally validated through in vitro assays (CCK-8, EdU, Transwell). SpliceSeq analysis revealed HDGF-mediated alternative splicing events in HCC.

RBP expression correlated significantly with HCC histological/diagnostic grades. Prognostic RBPs, enriched in ribosome biogenesis and rRNA processing pathways, were upregulated in specific cell clusters. Single-cell analysis revealed distinct RBP expression patterns between primary and early recurrent HCCs, nominating YRDC and HDGF as putative regulators. Myeloid-derived cell populations exhibited unique RBP profiles, suggesting crosstalk with malignant cells during HCC progression. In vitro assays suggested that HDGF may contribute to enhanced proliferation, migration, and invasion of HCC cells, whereas its knockdown attenuated these phenotypes. GO/KEGG analysis implicated HDGF in survival-associated alternative splicing events, supported by TCGA SpliceSeq data.

RBPs display single-cell-level heterogeneity and are associated with pathways relevant to HCC progression. HDGF is identified as a candidate oncogenic RBP based on in vitro phenotypes and correlative splicing analyses. These findings highlight the potential of RBPs, including HDGF, as candidates for further mechanistic and therapeutic exploration in HCC.